public void getMessages() {
RequestBuilder builder = new RequestBuilder(RequestBuilder.GET, URL.encode(URLGET));
try {
Request request =
builder.sendRequest(
null,
new RequestCallback() {
public void onError(Request request, Throwable exception) {}
public void onResponseReceived(Request request, Response response) {
if (200 == response.getStatusCode()) {
IResponse serverResponse = decodeJSON(response.getText());
processResponse(serverResponse);
} else {
Window.alert("Messages couldn't been recieved");
}
}
});
} catch (RequestException e) {
// Couldn't connect to server
}
}
public static void retrieveAncestors(final Event event, final PathHandler handler) {
String url = "/ReactomeRESTfulAPI/RESTfulWS/queryEventAncestors/" + event.getDbId();
RequestBuilder requestBuilder = new RequestBuilder(RequestBuilder.GET, url);
requestBuilder.setHeader("Accept", "application/json");
try {
requestBuilder.sendRequest(
null,
new RequestCallback() {
@Override
public void onResponseReceived(Request request, Response response) {
try {
JSONArray list = JSONParser.parseStrict(response.getText()).isArray();
Ancestors ancestors = new Ancestors(list);
List<Path> paths =
getPathsWithoutOrphanPathways(ancestors.getPathsContaining(event));
handler.onPathsRetrieved(paths);
} catch (Exception ex) {
// ToDo: Look into new Error Handling
}
}
@Override
public void onError(Request request, Throwable exception) {
// ToDo: Look into new Error Handling
}
});
} catch (RequestException ex) {
// ToDo: Look into new Error Handling
}
}
public static void fbLogin(String profileId) throws RequestException {
RequestBuilder builder =
new RequestBuilder(
RequestBuilder.POST, "http://localhost:8080/j_spring_service_security_check");
builder.setHeader("Content-type", "application/x-www-form-urlencoded");
builder.sendRequest(
"profile_id=" + profileId + "&service_name=facebook",
new RequestCallback() {
@Override
public void onResponseReceived(Request request, Response response) {
if (response.getStatusCode() < 400) {
History.newItem("photo");
}
}
@Override
public void onError(Request request, Throwable exception) {
return;
}
});
}
private void getAllTreeLessons() {
RequestBuilder builder = new RequestBuilder(RequestBuilder.GET, URLConstants.JSON_LESSONS);
try {
builder.sendRequest(
null,
new RequestCallback() {
public void onError(Request request, Throwable exception) {
displayError("Couldn't retrieve JSON : " + exception.getMessage());
}
public void onResponseReceived(Request request, Response response) {
if (Response.SC_OK == response.getStatusCode()) {
buildLessonTree(response);
} else {
displayError("Couldn't retrieve JSON (" + response.getStatusText() + ")");
}
}
});
} catch (RequestException e) {
displayError("Couldn't retrieve JSON : " + e.getMessage());
}
}
@Override
public void onReferencesRequired(final Long dbId) {
String url = "/ReactomeRESTfulAPI/RESTfulWS/queryReferences/" + dbId;
RequestBuilder requestBuilder = new RequestBuilder(RequestBuilder.GET, url);
requestBuilder.setHeader("Accept", "application/json");
try {
requestBuilder.sendRequest(
null,
new RequestCallback() {
@Override
public void onResponseReceived(Request request, Response response) {
try {
JSONArray list = JSONParser.parseStrict(response.getText()).isArray();
List<LiteratureReference> references = new ArrayList<LiteratureReference>();
for (int i = 0; i < list.size(); ++i) {
JSONObject object = list.get(i).isObject();
references.add((LiteratureReference) ModelFactory.getDatabaseObject(object));
}
DataRequiredListener.getDataRequiredListener()
.setRequiredReferences(dbId, references);
} catch (Exception ex) {
// ModelFactoryException, NullPointerException, IllegalArgumentException,
// JSONException
MessageObject msgObj =
new MessageObject(
"The received References object for 'DbId="
+ dbId
+ "' is empty or faulty and could not be parsed.\n"
+ "ERROR: "
+ ex.getMessage(),
getClass(),
MessageType.INTERNAL_ERROR);
eventBus.fireELVEvent(ELVEventType.INTERNAL_MESSAGE, msgObj);
Console.error(getClass() + " ERROR: " + ex.getMessage());
DataRequiredListener.getDataRequiredListener()
.setRequiredReferences(dbId, new ArrayList<LiteratureReference>());
}
}
@Override
public void onError(Request request, Throwable exception) {
if (!GWT.isScript()) {
Console.error(getClass() + " ERROR: " + exception.getMessage());
}
MessageObject msgObj =
new MessageObject(
"The request for 'DbId="
+ dbId
+ "' received an error instead of a valid response.\n"
+ "ERROR: "
+ exception.getMessage(),
getClass(),
MessageType.INTERNAL_ERROR);
eventBus.fireELVEvent(ELVEventType.INTERNAL_MESSAGE, msgObj);
DataRequiredListener.getDataRequiredListener()
.setRequiredReferences(dbId, new ArrayList<LiteratureReference>());
}
});
} catch (RequestException ex) {
MessageObject msgObj =
new MessageObject(
"The requested references data for 'DbId="
+ dbId
+ "' could not be received.\n"
+ "ERROR: "
+ ex.getMessage(),
getClass(),
MessageType.INTERNAL_ERROR);
eventBus.fireELVEvent(ELVEventType.INTERNAL_MESSAGE, msgObj);
Console.error(getClass() + " ERROR: " + ex.getMessage());
DataRequiredListener.getDataRequiredListener()
.setRequiredReferences(dbId, new ArrayList<LiteratureReference>());
}
}
@Override
public void onMoleculeDataRequired(final Molecule molecule) {
String url = "/ReactomeRESTfulAPI/RESTfulWS/queryById/ReferenceEntity/" + molecule.getDbId();
RequestBuilder requestBuilder = new RequestBuilder(RequestBuilder.GET, url);
requestBuilder.setHeader("Accept", "application/json");
try {
requestBuilder.sendRequest(
null,
new RequestCallback() {
@Override
public void onResponseReceived(Request request, Response response) {
try {
JSONObject json = JSONParser.parseStrict(response.getText()).isObject();
Molecule molecule =
new Molecule(ModelFactory.getDatabaseObject(json).getSchemaClass(), json);
DataRequiredListener.getDataRequiredListener().setRequiredMoleculeData(molecule);
} catch (Exception ex) {
// ModelFactoryException, NullPointerException, IllegalArgumentException,
// JSONException
MessageObject msgObj =
new MessageObject(
"The received object for Molecule '"
+ molecule.getDisplayName()
+ "' is empty or faulty and could not be parsed.\n"
+ "ERROR: "
+ ex.getMessage(),
getClass(),
MessageType.INTERNAL_ERROR);
eventBus.fireELVEvent(ELVEventType.INTERNAL_MESSAGE, msgObj);
Console.error(getClass() + " ERROR: " + ex.getMessage());
DataRequiredListener.getDataRequiredListener().setRequiredMoleculeData(molecule);
}
}
@Override
public void onError(Request request, Throwable exception) {
if (!GWT.isScript()) {
Console.error(getClass() + " ERROR: " + exception.getMessage());
}
MessageObject msgObj =
new MessageObject(
"The request for Molecule '"
+ molecule.getDisplayName()
+ "' received an error instead of a valid response.\n"
+ "ERROR: "
+ exception.getMessage(),
getClass(),
MessageType.INTERNAL_ERROR);
eventBus.fireELVEvent(ELVEventType.INTERNAL_MESSAGE, msgObj);
DataRequiredListener.getDataRequiredListener().setRequiredMoleculeData(molecule);
}
});
} catch (RequestException ex) {
MessageObject msgObj =
new MessageObject(
"The requested detailed data for Molecule \n'"
+ molecule.getDisplayName()
+ "' could not be received.\n"
+ "ERROR: "
+ ex.getMessage(),
getClass(),
MessageType.INTERNAL_ERROR);
eventBus.fireELVEvent(ELVEventType.INTERNAL_MESSAGE, msgObj);
Console.error(getClass() + " ERROR: " + ex.getMessage());
DataRequiredListener.getDataRequiredListener().setRequiredMoleculeData(molecule);
}
}
@Override
public void onPathRequired(final Event event) {
/* TODO Testing
but never used because DataRequiredListener is used by DetailsPanel and there ancestorsRequired is unused */
final long dbId = event.getDbId();
String url = "/ReactomeRESTfulAPI/RESTfulWS/queryEventAncestors/" + dbId;
RequestBuilder requestBuilder = new RequestBuilder(RequestBuilder.GET, url);
requestBuilder.setHeader("Accept", "application/json");
try {
requestBuilder.sendRequest(
null,
new RequestCallback() {
@Override
public void onResponseReceived(Request request, Response response) {
try {
JSONArray list = JSONParser.parseStrict(response.getText()).isArray();
Ancestors ancestors = new Ancestors(list);
DataRequiredListener.getDataRequiredListener()
.setRequiredAncestors(dbId, ancestors);
} catch (Exception ex) {
// ModelFactoryException, NullPointerException, IllegalArgumentException,
// JSONException
MessageObject msgObj =
new MessageObject(
"The received object for 'DbId="
+ event.getDbId()
+ "' is empty or faulty and could not be parsed into a path or hierarchy.\n"
+ "ERROR: "
+ ex.getMessage(),
getClass(),
MessageType.INTERNAL_ERROR);
eventBus.fireELVEvent(ELVEventType.INTERNAL_MESSAGE, msgObj);
Console.error(getClass() + " ERROR: " + ex.getMessage());
}
}
@Override
public void onError(Request request, Throwable exception) {
if (!GWT.isScript()) {
Console.error(getClass() + " ERROR: " + exception.getMessage());
}
MessageObject msgObj =
new MessageObject(
"The PathRequired request for 'DbId="
+ event.getDbId()
+ "' received an error instead of a valid response.\n"
+ "ERROR: "
+ exception.getMessage(),
getClass(),
MessageType.INTERNAL_ERROR);
eventBus.fireELVEvent(ELVEventType.INTERNAL_MESSAGE, msgObj);
}
});
} catch (RequestException ex) {
MessageObject msgObj =
new MessageObject(
"The requested data for 'DbId="
+ event.getDbId()
+ "' could not be received.\n"
+ "ERROR: "
+ ex.getMessage(),
getClass(),
MessageType.INTERNAL_ERROR);
eventBus.fireELVEvent(ELVEventType.INTERNAL_MESSAGE, msgObj);
Console.error(getClass() + " ERROR: " + ex.getMessage());
}
}
@Override
public void onDataRequired(final DatabaseObject databaseObject) {
final long dbId = databaseObject.getDbId();
String url = "/ReactomeRESTfulAPI/RESTfulWS/detailedView/DatabaseObject/" + dbId;
RequestBuilder requestBuilder = new RequestBuilder(RequestBuilder.GET, url);
requestBuilder.setHeader("Accept", "application/json");
try {
requestBuilder.sendRequest(
null,
new RequestCallback() {
@Override
public void onResponseReceived(Request request, Response response) {
try {
JSONObject json = JSONParser.parseStrict(response.getText()).isObject();
DatabaseObject databaseObject = ModelFactory.getDatabaseObject(json);
DataRequiredListener.getDataRequiredListener()
.setRequiredData(dbId, databaseObject);
eventBus.fireELVEvent(ELVEventType.DETAILED_VIEW_LOADED, databaseObject);
} catch (Exception ex) {
// ModelFactoryException, NullPointerException, IllegalArgumentException,
// JSONException
MessageObject msgObj =
new MessageObject(
"The received object for 'DbId="
+ databaseObject.getDbId()
+ "' is empty or faulty and could not be parsed.\n"
+ "ERROR: "
+ ex.getMessage(),
getClass(),
MessageType.INTERNAL_ERROR);
eventBus.fireELVEvent(ELVEventType.INTERNAL_MESSAGE, msgObj);
Console.error(getClass() + " ERROR: " + ex.getMessage());
}
}
@Override
public void onError(Request request, Throwable exception) {
if (!GWT.isScript()) {
Console.error(getClass() + " ERROR: " + exception.getMessage());
}
MessageObject msgObj =
new MessageObject(
"The request for 'DbId="
+ databaseObject.getDbId()
+ "' received an error instead of a valid response.\n"
+ "ERROR: "
+ exception.getMessage(),
getClass(),
MessageType.INTERNAL_ERROR);
eventBus.fireELVEvent(ELVEventType.INTERNAL_MESSAGE, msgObj);
}
});
} catch (RequestException ex) {
MessageObject msgObj =
new MessageObject(
"The requested data for 'DbId="
+ databaseObject.getDbId()
+ "' could not be received.\n"
+ "ERROR: "
+ ex.getMessage(),
getClass(),
MessageType.INTERNAL_ERROR);
eventBus.fireELVEvent(ELVEventType.INTERNAL_MESSAGE, msgObj);
Console.error(getClass() + " ERROR: " + ex.getMessage());
}
}
protected void performOperation(boolean feedback) {
final String url = GWT.getHostPageBaseURL() + "api/version/softwareUpdates"; // $NON-NLS-1$
RequestBuilder requestBuilder = getRequestBuilder(RequestBuilder.GET, url);
requestBuilder.setHeader("If-Modified-Since", "01 Jan 1970 00:00:00 GMT");
requestBuilder.setHeader("accept", "text/plain");
try {
requestBuilder.sendRequest(
null,
new RequestCallback() {
public void onError(Request request, Throwable exception) {
MessageDialogBox dialogBox =
new MessageDialogBox(
Messages.getString("softwareUpdates"),
Messages.getString("noUpdatesAvailable"),
false,
false,
true); //$NON-NLS-1$ //$NON-NLS-2$
dialogBox.center();
}
public void onResponseReceived(Request request, Response response) {
Document doc = XMLParser.parse(response.getText());
NodeList updates = doc.getElementsByTagName("update"); // $NON-NLS-1$
if (updates.getLength() > 0) {
FlexTable updateTable = new FlexTable();
updateTable.setStyleName("backgroundContentTable"); // $NON-NLS-1$
updateTable.setWidget(
0, 0, new Label(Messages.getString("version"))); // $NON-NLS-1$
updateTable.setWidget(0, 1, new Label(Messages.getString("type"))); // $NON-NLS-1$
updateTable.setWidget(0, 2, new Label(Messages.getString("os"))); // $NON-NLS-1$
updateTable.setWidget(0, 3, new Label(Messages.getString("link"))); // $NON-NLS-1$
updateTable
.getCellFormatter()
.setStyleName(0, 0, "backgroundContentHeaderTableCell"); // $NON-NLS-1$
updateTable
.getCellFormatter()
.setStyleName(0, 1, "backgroundContentHeaderTableCell"); // $NON-NLS-1$
updateTable
.getCellFormatter()
.setStyleName(0, 2, "backgroundContentHeaderTableCell"); // $NON-NLS-1$
updateTable
.getCellFormatter()
.setStyleName(0, 3, "backgroundContentHeaderTableCellRight"); // $NON-NLS-1$
for (int i = 0; i < updates.getLength(); i++) {
Element updateElement = (Element) updates.item(i);
String version = updateElement.getAttribute("version"); // $NON-NLS-1$
String type = updateElement.getAttribute("type"); // $NON-NLS-1$
String os = updateElement.getAttribute("os"); // $NON-NLS-1$
// String title = updateElement.getAttribute("title");
String downloadURL =
updateElement
.getElementsByTagName("downloadurl")
.item(0)
.toString(); //$NON-NLS-1$
downloadURL =
downloadURL.substring(
downloadURL.indexOf("http"),
downloadURL.indexOf("]")); // $NON-NLS-1$ //$NON-NLS-2$
updateTable.setWidget(i + 1, 0, new Label(version));
updateTable.setWidget(i + 1, 1, new Label(type));
updateTable.setWidget(i + 1, 2, new Label(os));
updateTable.setWidget(
i + 1,
3,
new HTML(
"<A HREF=\""
+ downloadURL
+ "\" target=\"_blank\" title=\""
+ downloadURL
+ "\">"
+ Messages.getString("download")
+ "</A>")); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$ //$NON-NLS-4$
// //$NON-NLS-5$
updateTable
.getCellFormatter()
.setStyleName(i + 1, 0, "backgroundContentTableCell"); // $NON-NLS-1$
updateTable
.getCellFormatter()
.setStyleName(i + 1, 1, "backgroundContentTableCell"); // $NON-NLS-1$
updateTable
.getCellFormatter()
.setStyleName(i + 1, 2, "backgroundContentTableCell"); // $NON-NLS-1$
updateTable
.getCellFormatter()
.setStyleName(i + 1, 3, "backgroundContentTableCellRight"); // $NON-NLS-1$
if (i == updates.getLength() - 1) {
// last
updateTable
.getCellFormatter()
.setStyleName(i + 1, 0, "backgroundContentTableCellBottom"); // $NON-NLS-1$
updateTable
.getCellFormatter()
.setStyleName(i + 1, 1, "backgroundContentTableCellBottom"); // $NON-NLS-1$
updateTable
.getCellFormatter()
.setStyleName(i + 1, 2, "backgroundContentTableCellBottom"); // $NON-NLS-1$
updateTable
.getCellFormatter()
.setStyleName(
i + 1, 3, "backgroundContentTableCellBottomRight"); // $NON-NLS-1$
}
}
PromptDialogBox versionPromptDialog =
new PromptDialogBox(
Messages.getString("softwareUpdateAvailable"),
Messages.getString("ok"),
null,
false,
true,
updateTable); //$NON-NLS-1$ //$NON-NLS-2$
versionPromptDialog.center();
} else {
MessageDialogBox dialogBox =
new MessageDialogBox(
Messages.getString("softwareUpdates"),
Messages.getString("noUpdatesAvailable"),
false,
false,
true); //$NON-NLS-1$ //$NON-NLS-2$
dialogBox.center();
}
}
});
} catch (RequestException e) {
Window.alert(e.getMessage());
// showError(e);
}
}
@Override
public void onResourceChosen(final String resource) {
String url = AnalysisHelper.URL_PREFIX + "/token/" + token + "?page=1&resource=" + resource;
RequestBuilder requestBuilder = new RequestBuilder(RequestBuilder.GET, url);
requestBuilder.setHeader("Accept", "application/json");
try {
requestBuilder.sendRequest(
null,
new RequestCallback() {
@Override
public void onResponseReceived(Request request, Response response) {
try {
AnalysisResult result =
AnalysisModelFactory.getModelObject(AnalysisResult.class, response.getText());
// We have to do this here because there is no name coming from the RESTFul service
result
.getSummary()
.setSpeciesName(speciesMap.get(result.getSummary().getSpecies()));
view.clearSelection();
view.showResult(result, resource);
view.selectPathway(selected);
} catch (AnalysisModelException e) {
MessageObject msgObj =
new MessageObject(
"The received object for '"
+ resource
+ "' is empty or faulty and could not be parsed.\n"
+ "ERROR: "
+ e.getMessage(),
getClass(),
MessageType.INTERNAL_ERROR);
eventBus.fireELVEvent(ELVEventType.INTERNAL_MESSAGE, msgObj);
Console.error(getClass() + " ERROR: " + e.getMessage());
view.setInitialState();
}
}
@Override
public void onError(Request request, Throwable exception) {
// TODO Check before commit - not yet tested
MessageObject msgObj =
new MessageObject(
"The request for '"
+ resource
+ "' received an error instead of a valid response.\n"
+ "ERROR: "
+ exception.getMessage(),
getClass(),
MessageType.INTERNAL_ERROR);
eventBus.fireELVEvent(ELVEventType.INTERNAL_MESSAGE, msgObj);
Console.error(getClass() + " ERROR: " + exception.getMessage());
view.setInitialState();
}
});
} catch (RequestException ex) {
MessageObject msgObj =
new MessageObject(
"The requested detailed data for '"
+ resource
+ "'\nin the Analysis could not be received.\n"
+ "ERROR: "
+ ex.getMessage(),
getClass(),
MessageType.INTERNAL_ERROR);
eventBus.fireELVEvent(ELVEventType.INTERNAL_MESSAGE, msgObj);
Console.error(getClass() + " ERROR: " + ex.getMessage());
view.setInitialState();
}
}
